Discovery in the Post-Genomic Age
How to use proteomic assays to discover more and publish faster
Introduction ELISA, or enzyme-linked immunosorbent assay, is the “gold standard” method for protein detection.1 In this blog, three popular ELISA platforms are reviewed: standard ELISA, immuno-PCR, and single molecule array (SIMOA). These ELISAs will be compared regarding their design principles, sample volumes, instruments, and sensitivities. How ELISA works The basic…
Introduction A microarray is an assay that enables the simultaneous detection of multiple molecules, such as nucleic acids, peptides, proteins, or antibodies. They are called “micro”-arrays because the analytes are measured within a small surface area; for example, thousands of molecules can be analyzed on a standard glass slide (75…
Introduction Publications are the cornerstone of science. They disseminate data that expand our understanding of the world around us (and beyond!) and help secure funding for additional studies. However, most manuscripts do not pass the journal’s initial editorial process. Here, we review the editorial process and provide 5 steps for…
Like other coronaviruses, the genome of SARS-CoV-2 contains ten or more open reading frames (ORFs) encoding some 29 proteins. Roughly two thirds of the viral RNA are contained within the first two, called ORF1a and ORF1b. [1] These are translated into two large non-structural polypeptides (NSPS) that are then cleaved…
Introduction The coronavirus disease 2019 (COVID-19) is caused by the highly contagious SARS-CoV-2 virus. [1] Some infected individuals are asymptomatic while others experience very severe symptoms that can result in death (Figure 1). [2] More specifically, those over 55 years old or have underlying conditions are especially vulnerable to developing…
Introduction In December 2019, the first cases of patients with severe acute respiratory syndrome (SARS) caused by the novel coronavirus, SARS-CoV-2, were reported in China. [1] In mid-March 2020, the World Health Organization (WHO) declared COVID-19 (COronaVIrus Disease of 2019) a pandemic. By mid-May 2020, there were ~4.5 million confirmed…
Introduction Protein phosphorylation is the most well-studied post translational modification (PTM), in which a phosphoryl group from adenosine triphosphate (ATP) is covalently attached to a serine (~86%), threonine (~12%), or tyrosine (~2%) by a kinase and removed by a phosphatase (Figure 1). [1] Phosphorylation at other amino acids have also…
Introduction Proteins play an integral role in human health. As such, basic, applied, and clinical research aim to understand how protein expression, localization, post translational modifications (PTMs), and interactions regulate homeostasis and disease (see yellow box). Our current understanding of how proteins affect cellular phenotype is based on numerous applications,…
Highlights Antibody arrays: removal of high abundance proteins is not required, but antibody availability limits protein detection. Mass spectrometry: “hypothesis-free” protein detection is affected by high abundance proteins and peptide ionization. Both high throughput technologies are capable of semi-quantitative and quantitative data. Antibody arrays and mass spectrometry complement each other.…
What is it? Random forest consists of hundreds or more decision trees, with each tree using a random subset of data. All of the decision trees cast a vote on the classification of a sample; the majority vote wins. When is it used? This analysis is one of the most…